Application Runs, Won't Quit Or Force Quit... Ideas?

Issue: My computer has been running slow and now I have been having issues with the applications. I will launch an application (such as Firefox or Mail) and it runs fine. I then try to quit the application and the window will close. The application does not completely quit. I can still see it active in the Dock and it appears when I try to Force Quit it. The application will not Force Quit and the wheel begins to spin. If I hold down the power button on the front, turn it off and fire it up again, the application can launch again. The same thing happens again and again.
I have been trying to figure this one out for a week now. I Repaired Permissions, ran Disk Warrior & Tech Tools, booted off the install disk and ran Disk Utilities. I am still having the problem. I haven't installed any new software or hardware. Disk Warrior and Tech Tools did not find any problems. I have two drives mirrored with Soft Raid. I also have an external drive that I use Time Machine to back up my files. I have disconnected all external drives while troubleshooting, but have not achieved success yet. I read through some posts here, but didn't find exactly what my situation was. Any ideas?

Delete these guys:
/Library/Caches
/System/Library/Caches
no harm.
If you do a full backup with SD, why not restore it then to another location? test the water so to speak.
Yes, if you have a mirror you would have to redo. SoftRAID is easy to deal with, and you can have 2 or even 3 drive mirror (with stripped reads). I rebuild RAIDs frequently, anytime there is a major change to OS (10.4.4 was just such a change, too, along with 10.5.0, .2, not just major point numbers)
Restore with SuperDuper should be identical to how things were configured.
Always keep two backup sets.
Have a TEST system for sure.
SD runs as sudo administrator so every user's account should backup and restore properly. Double check your settings. This is not reinstall.
Practice trial run. Never do a "live test" if you don't want to face the music.

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